Meat is a crucial part of a balanced diet, the environment secretary has said, as he told farmers about his “health and harmony” vision for food.

Michael Gove’s new vision for British agriculture post-Brexit envisages farmers playing a critical role in improving public health.

“There is a growing public interest in the impact of our current diet on our health,” he said. Non-communicable diseases such as heart and lung disease, cancer and diabetes accounted for 89% of deaths in the UK in 2014, according to the World Health Organization, he pointed out, and a major driver of that has been our diet: “the wrong fats, sugar, salt and other additives form too large a part of our national diet”.

Improving our national diet is an important job for our farmers, he told the audience: “A balanced diet, rich in fresh fruit and vegetables, beans, pulses and cereals, fresh dairy produce and protein sources such as fresh fish, offal and properly sourced meat is critical to human health and flourishing.”

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Asked by the Guardian if, given the known environmental impacts of livestock farming, the government might consider suggesting that people reduce their meat consumption, Gove said: “For health reasons there’s an appropriate level of meat in anyone’s diet which doctors and nutritionists would advise us to consume.”

“It’s not my job to micro-manage what goes into a shopping basket,” he added, “but while I respect the rights of people who might be vegan or vegetarian to make that choice, nevertheless I don’t think anyone should be shy or abashed in drawing attention to the fact that livestock farming contributes to the mixed farming methods that provide a specific set of farming benefits and that mixed farming and meat is part of a balanced diet.”

But the discussion over whether humans need meat as a protein source is profoundly polarised. There is also much discussion over the health impacts of our current levels of meat consumption compared to predominantly plant-based diets.

Gove plans to redesign the farming subsidy system so farmers are paid for environmental services such as improving soils and levels of biodiversity, viewing Brexit as a unique opportunity. He faces an anxious sector with concerns ranging from falling incomes due to cheap food prices and international competition, to environmental issues like declining soil health.

The decline in numbers of small abattoirs was raised, and the challenges this presents to farmers around the country. Gove said there were discussions about how animals could be killed closer to where they were raised. He also spoke about plans to change labelling systems, saying: “I don’t want to take anything away from the work of Red Tractor and Leaf, but we can go further and develop a gold standard system of labelling.”

Richard Young of the Sustainable Food Trust said: “We would argue that people should reduce their consumption of grain-fed meats. Two-thirds of British farmland is only suitable for grass.” Fully grass-fed cattle, the trust argues, can make a useful environmental contribution.